text: // Author: David Alexander
  
  //
  // Linear-space basic alignment following Hirschberg
  //
  
  #ifndef PBCOPPER_ALIGN_LINEARALIGNMENT_H
  #define PBCOPPER_ALIGN_LINEARALIGNMENT_H
  
  #include <string>
  
  #include <pbcopper/align/PairwiseAlignment.h>
  
  namespace PacBio {
  namespace Align {
  
  class PairwiseAlignment;
  
  PairwiseAlignment* AlignLinear(const std::string& target, const std::string& query,
                                 AlignConfig config = AlignConfig::Default());
  
  PairwiseAlignment* AlignLinear(const std::string& target, const std::string& query, int* score,
                                 AlignConfig config = AlignConfig::Default());
  
  }  // namespace Align
  }  // namespace PacBio
  
  #endif  // PBCOPPER_ALIGN_LINEARALIGNMENT_H
  